Last updated: 2018-09-10

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    Untracked:  analysis/drugheatmap.pdf
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    Untracked:  analysis/drugheatmap_target_color.pdf
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File	Version	Author	Date	Message
Rmd	37313f4	bingrus	2018-09-10	wflow_git_commit(“analysis/drugcorr.Rmd”)

drug correlation analysis with target sets

method

scale the microarrary expression data for each sample to z-score accross all genes
do ssgsea on the converted microarray expression data
compute correlation scores for ssgsea score to the drug response data (IC50)

Result 1: drug correlation analysis with targets sets

pdf figure with dendogram

Expand here to see past versions of drugheatmap_target.pdf:

Version	Author	Date
c24d8ce	bingrus	2018-09-10

interactive figure without dendogram (same order)

interactive figure with target set class labels

interactive figure with regulator age labels

Result 2: the information on the cluster drugs

	Target.s.	Mechanism.of.action	Class	group
17-AAG	HSP90	Heat Shock Protein 90 (hsp90) Inhibitor	Other targeted therapies	1
AZD0530	Src, Abl/Bcr-Abl, EGFR	Src and Abl inhibitor	Kinase inhibitor	1
Erlotinib	EGFR	EGFR Inhibitor	Kinase inhibitor	1
Lapatinib	EGFR, HER2	EGFR and HER2 Inhibitor	Kinase inhibitor	1
ZD-6474	Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	1
AEW541	IGF-1R	IGF-1R Inhibitor	Kinase inhibitor	2
L-685458	Gamma Secretase	gamma-Secretase Inhibitor	Other targeted therapies	2
Paclitaxel	beta-tubulin	Microtubule-Stabilizing Agents	Cytotoxic	2
Panobinostat	HDAC	Histone Deacetylase (HDAC) Inhibitor	Other targeted therapies	2
Sorafenib	Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	2
TAE684	ALK	ALK Inhibitor	Kinase inhibitor	2
AZD6244	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	3
PD-0325901	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	3
PLX4720	RAF	Raf kinase B Inhibitor	Kinase inhibitor	3
Irinotecan	Topoisomerase I	NA	NA	4
Nutlin-3	MDM2	MDM2 Inhibitor	Other targeted therapies	4
PF2341066	c-MET, ALK	c-MET and ALK Inhibitor	Kinase inhibitor	4
RAF265	Raf kinase B, KDR	Raf kinase B and KDR Inhibitor	Kinase inhibitor	4
TKI258	EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR	Multi-kinase inhibitor	Kinase inhibitor	4
Topotecan	Topoisomerase I	DNA Topoisomerase I Inhibitor	Cytotoxic	4
LBW242	IAP	Inhibitor of Apoptosis Proteins (IAP) Inhibitor	Other targeted therapies	5
Nilotinib	Abl/Bcr-Abl	Abl Inhibitor	Kinase inhibitor	5
PD-0332991	CDK4/6	CDK4/6 Inhibitor	Kinase inhibitor	5
PHA-665752	c-MET	c-MET Inhibitor	Kinase inhibitor	5

Session information

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] kableExtra_0.9.0     knitr_1.20           GSEABase_1.42.0     
 [4] graph_1.58.0         annotate_1.58.0      XML_3.98-1.16       
 [7] AnnotationDbi_1.42.1 IRanges_2.14.11      S4Vectors_0.18.3    
[10] GSVA_1.28.0          heatmaply_0.15.2     viridis_0.5.1       
[13] viridisLite_0.3.0    plotly_4.8.0         ggplot2_3.0.0       
[16] dplyr_0.7.6          gplots_3.0.1         GEOquery_2.48.0     
[19] Biobase_2.40.0       BiocGenerics_0.26.0  reshape_0.8.7       

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2    class_7.3-14        modeltools_0.2-22  
  [4] mclust_5.4.1        rprojroot_1.3-2     rstudioapi_0.7     
  [7] flexmix_2.3-14      bit64_0.9-7         mvtnorm_1.0-8      
 [10] xml2_1.2.0          codetools_0.2-15    R.methodsS3_1.7.1  
 [13] robustbase_0.93-2   geneplotter_1.58.0  shinythemes_1.1.1  
 [16] jsonlite_1.5        workflowr_1.1.1     cluster_2.0.7-1    
 [19] kernlab_0.9-27      R.oo_1.22.0         shiny_1.1.0        
 [22] readr_1.1.1         compiler_3.5.0      httr_1.3.1         
 [25] backports_1.1.2     assertthat_0.2.0    lazyeval_0.2.1     
 [28] limma_3.36.3        later_0.7.3         htmltools_0.3.6    
 [31] tools_3.5.0         bindrcpp_0.2.2      gtable_0.2.0       
 [34] glue_1.3.0          reshape2_1.4.3      Rcpp_0.12.18       
 [37] trimcluster_0.1-2.1 gdata_2.18.0        crosstalk_1.0.0    
 [40] iterators_1.0.10    fpc_2.1-11.1        stringr_1.3.1      
 [43] rvest_0.3.2         mime_0.5            gtools_3.8.1       
 [46] dendextend_1.8.0    DEoptimR_1.0-8      MASS_7.3-50        
 [49] scales_1.0.0        TSP_1.1-6           hms_0.4.2          
 [52] promises_1.0.1      RColorBrewer_1.1-2  yaml_2.2.0         
 [55] memoise_1.1.0       gridExtra_2.3       stringi_1.2.4      
 [58] RSQLite_2.1.1       highr_0.7           gclus_1.3.1        
 [61] foreach_1.4.4       seriation_1.2-3     caTools_1.17.1.1   
 [64] rlang_0.2.2         pkgconfig_2.0.2     prabclus_2.2-6     
 [67] bitops_1.0-6        evaluate_0.11       lattice_0.20-35    
 [70] purrr_0.2.5         bindr_0.1.1         labeling_0.3       
 [73] htmlwidgets_1.2     bit_1.1-14          tidyselect_0.2.4   
 [76] plyr_1.8.4          magrittr_1.5        R6_2.2.2           
 [79] DBI_1.0.0           pillar_1.3.0        whisker_0.3-2      
 [82] withr_2.1.2         RCurl_1.95-4.11     nnet_7.3-12        
 [85] tibble_1.4.2        crayon_1.3.4        KernSmooth_2.23-15 
 [88] rmarkdown_1.10      grid_3.5.0          data.table_1.11.4  
 [91] blob_1.1.1          git2r_0.23.0        digest_0.6.16      
 [94] diptest_0.75-7      webshot_0.5.0       xtable_1.8-3       
 [97] tidyr_0.8.1         httpuv_1.4.5        R.utils_2.7.0      
[100] munsell_0.5.0       registry_0.5

This reproducible R Markdown analysis was created with workflowr 1.1.1

Drug correlation